Some resources and other good programs for enhancer analysis
- BioEdit
- A full-featured multiple alignment manipulation program,
which I use for all of my manual enhancer adjustments.
- GenePalette - An
easy-to-use gene browser that supports annotation of all kinds
of features. I took a great deal of inspiration from Mark's
design.
- RSA-Tools - A large suite
of tools for analyzing regulatory sequences, several of which
inspired Twine features.
- Galaxy - Lots of
great tools for sequence manipulation and analysis, especially
on the genome scale.
- Dialign-TX
- My personal favorite sequence alignment software, although
many others do just fine. It can be a bit of a struggle to
compile and install on Windows machines, but there are also web servers available.
- Phylogibbs-MP
- A great Gibbs Sampling motif finder that incorporates
phylogenetic conservation into statistics.
- MEME - A large
collection of motif discovery and comparison tools. The utility
for creating Markov Background files can be obtained here.
- TFDBS - Binding
matrices for a large number of Drosophila transcription
factors, derived from Bacterial One-hybrid assays.
- Jaspar and Transfac
- Large collections of binding site info for lots of
transcription factors.
Other Java programs that I've written
- DesktopTimer
- does all the stuff your real scientific timer does (and a
bit more).